tbuckley/cabot-search huggingface dataset:
Finding consistency in classifications of myeloid neoplasms: a perspective on behalf of the International Workshop for Myelodysplastic Syndromes
Authors: Amer M. Zeidan, Jan Philipp Bewersdorf, Rena Buckstein, Mikkael A. Sekeres, David P. Steensma, Uwe Platzbecker, Sanam Loghavi, Jacqueline Boultwood, Rafael Bejar, John M. Bennett, Uma Borate, Andrew M. Brunner, Hetty Carraway, Jane E. Churpek, Naval G. Daver, Matteo Della Porta, Amy E. DeZern, Fabio Efficace, Pierre Fenaux, Maria E. Figueroa, Peter Greenberg, Elizabeth A. Griffiths, Stephanie Halene, Robert P. Hasserjian, Christopher S. Hourigan, Nina Kim, Tae Kon Kim, Rami S. Komrokji, Vijay Kutchroo, Alan F. List, Richard F. Little, Ravi Majeti, Aziz Nazha, Stephen D. Nimer, Olatoyosi Odenike, Eric Padron, Mrinal M. Patnaik, Gail J. Roboz, David A. Sallman, Guillermo Sanz, Maximilian Stahl, Daniel T. Starczynowski, Justin Taylor, Zhuoer Xie, Mina Xu, Michael R. Savona, Andrew H. Wei, Omar Abdel-Wahab, Valeria Santini
Journal: Leukemia (2022)
Genome sequencing reveals evidence of adaptive variation in the genus Zea
Authors: Lu Chen, Jingyun Luo, Minliang Jin, Ning Yang, Xiangguo Liu, Yong Peng, Wenqiang Li, Alyssa Phillips, Brenda Cameron, Julio S. Bernal, Rubén Rellán-Álvarez, Ruairidh J. H. Sawers, Qing Liu, Yuejia Yin, Xinnan Ye, Jiali Yan, Qinghua Zhang, Xiaoting Zhang, Shenshen Wu, Songtao Gui, Wenjie Wei, Yuebin Wang, Yun Luo, Chenglin Jiang, Min Deng, Min Jin, Liumei Jian, Yanhui Yu, Maolin Zhang, Xiaohong Yang, Matthew B. Hufford, Alisdair R. Fernie, Marilyn L. Warburton, Jeffrey Ross-Ibarra, Jianbing Yan
Journal: Nature Genetics (2022)
Closed-loop optogenetic control of the dynamics of neural activity in non-human primates
Authors: B. Zaaimi, M. Turnbull, A. Hazra, Y. Wang, C. Gandara, F. McLeod, E. E. McDermott, E. Escobedo-Cousin, A. Shah Idil, R. G. Bailey, S. Tardio, A. Patel, N. Ponon, J. Gausden, D. Walsh, F. Hutchings, M. Kaiser, M. O. Cunningham, G. J. Clowry, F. E. N. LeBeau, T. G. Constandinou, S. N. Baker, N. Donaldson, P. Degenaar, A. O’Neill, A. J. Trevelyan, A. Jackson
Journal: Nature Biomedical Engineering (2022)
Early-life and health behaviour influences on lung function in early adulthood
Authors: Osama Mahmoud, Raquel Granell, Gabriela P. Peralta, Judith Garcia-Aymerich, Deborah Jarvis, John Henderson, Jonathan Sterne
Journal: European Respiratory Journal (2022)

Rationale Early-life exposures may influence lung function at different stages of the life course. However, the relative importance of characteristics at different stages of infancy and childhood are unclear. Objectives To examine the associations and relative importance of early-life events on lung function at age 24 years. Methods We followed 7545 children from the Avon Longitudinal Study of Parents and Children from birth to 24 years. Using previous knowledge, we classified an extensive list of putative risk factors for low lung function, covering sociodemographic, environmental, lifestyle and physiological characteristics, according to timing of exposure: 1) demographic, maternal and child; 2) perinatal; 3) postnatal; 4) early childhood; and 5) adolescence characteristics. Lung function measurements (forced vital capacity (FVC), forced expiratory volume in 1 s (FEV 1 ), FEV 1 /FVC and forced expiratory flow at 25–75% of FVC) were standardised for sex, age and height. The proportion of the remaining variance explained by each characteristic was calculated. The association and relative importance (RI) of each characteristic for each lung function measure was estimated using linear regression, adjusted for other characteristics in the same and previous categories. Results Lower maternal perinatal body mass index (BMI), lower birthweight, lower lean mass and higher fat mass in childhood had the largest RI (0.5–7.7%) for decreased FVC. Having no siblings, lower birthweight, lower lean mass and higher fat mass were associated with decreased FEV 1 (RI 0.5–4.6%). Higher lean mass and childhood asthma were associated with decreased FEV 1 /FVC (RI 0.6–0.8%). Conclusions Maternal perinatal BMI, birthweight, childhood lean and fat mass and early-onset asthma are the factors in infancy and childhood that have the greatest influence on early-adult lung function.
The aminoglycoside-modifying enzyme Eis2 represents a new potential<i>in vivo</i>target for reducing antimicrobial drug resistance in<i>Mycobacterium abscessus</i>complex
Authors: Nicola Ivan Lorè, Fabio Saliu, Andrea Spitaleri, Daniel Schäfle, Francesca Nicola, Daniela Maria Cirillo, Peter Sander
Journal: European Respiratory Journal (2022)

<b>This study identified innovative therapeutic targets to reinforce existing current antibiotic treatments against <i>M. abscessus</i> complex, exploiting a murine preclinical model of respiratory infection and 727 publicly available genomes from clinical isolates</b> https://bit.ly/3eD4Pja
Efficacy of three COVID-19 vaccine doses in lung transplant recipients: a multicentre cohort study
Authors: Gaëlle Dauriat, Laurence Beaumont, Liem Binh Luong Nguyen, Benjamin Renaud Picard, Morgane Penhouet, Benjamin Coiffard, Mathilde Salpin, Xavier Demant, Christel Saint Raymond, Nicolas Carlier, Jonathan Messika, Martine Reynaud Gaubert, Isabelle Danner, Floriane Gallais, Antoine Roux, Jérôme Le Pavec
Journal: European Respiratory Journal (2022)

Question addressed by the study Do three coronavirus disease 2019 (COVID-19) vaccine doses induce a serological response in lung transplant recipients? Methods We retrospectively included 1071 adults (551 (52%) males) at nine transplant centres in France. Each had received three COVID-19 vaccine doses in 2021, after lung transplantation. An anti-spike protein IgG response, defined as a titre &gt;264 BAU·mL −1 after the third dose (median (interquartile range (IQR)) 3.0 (1.7–4.1) months), was the primary outcome and adverse events were the secondary outcomes. Median (IQR) age at the first vaccine dose was 54 (40–63) years and median (IQR) time from transplantation to the first dose was 64 (30–110) months. Results Median (IQR) follow-up after the first dose was 8.3 (6.7–9.3) months. A vaccine response developed in 173 (16%) patients. Factors independently associated with a response were younger age at vaccination, longer time from transplantation to vaccination and absence of corticosteroid or mycophenolate therapy. After vaccination, 51 (5%) patients (47 non-responders (47/898 (5%)) and four (4/173 (2%)) responders) experienced COVID-19, at a median (IQR) of 6.6 (5.1–7.3) months after the third dose. No responders had severe COVID-19 compared with 15 non-responders, including six who died of the disease. Conclusions Few lung transplant recipients achieved a serological response to three COVID-19 vaccine doses, indicating a need for other protective measures. Older age and use of mycophenolate or corticosteroids were associated with absence of a response. The low incidence of COVID-19 might reflect vaccine protection via cellular immunity and/or good adherence to shielding measures.
3D (bio)printing of lungs: past, present, and future
Authors: Mohammadhossein Dabaghi, Mabel Barreiro Carpio, Jose Manuel Moran-Mirabal, Jeremy Alexander Hirota
Journal: European Respiratory Journal (2022)

<b>The field of 3D bioprinting is rapidly evolving, and the lung is not being left behind. Interdisciplinary advances in 3D printing technology, bioink formulations, and cell biology are moving closer towards faithfully recapitulating the native human lung.</b>https://bit.ly/3EL3XUe
What next for covid-19 vaccines?: Video 1
Authors: Mun-Keat Looi, Elisabeth Mahase
Journal: BMJ (2022)

What next for covid-19 vaccines?As omicron booster jabs are approved and rolled out for the first time, The BMJ asks how vaccines will evolve as we learn to live with the virus Mun-Keat Looi, Elisabeth MahaseWill we continue to need annual covid boosters?
METTL3 mediates chemoresistance by enhancing AML homing and engraftment via ITGA4
Authors: Mingying Li, Jingjing Ye, Yuan Xia, Meng Li, Guosheng Li, Xiang Hu, Xiuhua Su, Dongmei Wang, Xin Zhao, Fei Lu, Jingxin Li, Daoxin Ma, Tao Sun, Chunyan Ji
Journal: Leukemia (2022)

Chemoresistant leukemia relapse is one of the most common causes of death for acute myeloid leukemia (AML) patients and the homing/engraftment in bone marrow (BM) are crucial steps for AML cells to acquire chemoresistance by interacting with stromal cell components. No crosstalk between m6A modification and homing/engraftment has been reported. Here, we performed comprehensive high-throughput analyses, including RNA sequencing of CR (complete remission) and relapsed AML patients, and reverse-phase protein arrays of chemoresistant cells to identify METTL3 as a key player regulating AML chemoresistance. Then, METTL3-mediated m6A modification was proved to induce the chemoresistance in vitro and in vivo. Furthermore, AML homing/engraftment was discovered being enhanced by upregulated-METTL3 in chemoresistant cells. And the homing/engraftment and drug-resistance associated phenotypes of chemoresistant cells could be reversed by a METTL3 inhibitor. Mechanistically, METTL3 extended the half-life of ITGA4 mRNA by m6A methylation, and then, increased expression of ITGA4 protein to enhance homing/engraftment of AML cells. The results provide insights into the function of m6A modification on the interaction between AML cells and BM niches and clarify the relationship between METTL3 and AML homing/engraftment, suggesting a therapeutic strategy for the treatment of refractory/relapsed AML with METTL3 inhibitors.
Hyperdiploidy: the longest known, most prevalent, and most enigmatic form of acute lymphoblastic leukemia in children
Authors: Oskar A. Haas, Arndt Borkhardt
Journal: Leukemia (2022)

Hyperdiploidy is the largest genetic entity B-cell precursor acute lymphoblastic leukemia in children. The diagnostic hallmark of its two variants that will be discussed in detail herein is a chromosome count between 52 and 67, respectively. The classical HD form consists of heterozygous di-, tri-, and tetrasomies, whereas the nonclassical one (usually viewed as "duplicated hyperhaploid") contains only disomies and tetrasomies. Despite their apparently different clinical behavior, we show that these two sub-forms can in principle be produced by the same chromosomal maldistribution mechanism. Moreover, their respective array, gene expression, and mutation patterns also indicate that they are biologically more similar than hitherto appreciated. Even though in-depth analyses of the genomic intricacies of classical HD leukemias are indispensable for the elucidation of the disease process, the ensuing results play at present surprisingly little role in treatment stratification, a fact that can be attributed to the overall good prognoses and low relapse rates of the concerned patients and, consequently, their excellent treatment outcome. Irrespective of this underutilization, however, the detailed genetic characterization of HD leukemias may, especially in planned treatment reduction trials, eventually become important for further treatment stratification, patient management, and the clinical elucidation of outcome data. It should therefore become an integral part of all upcoming treatment studies.
Obstructive sleep apnoea is related to melanoma aggressiveness through paraspeckle protein-1 upregulation
Authors: Carolina Cubillos-Zapata, Miguel Ángel Martínez-García, Elena Díaz-García, Sara García-Tovar, Francisco Campos-Rodríguez, Manuel Sánchez-de-la-Torre, Eduardo Nagore, Antonio Martorell-Calatayud, Luis Hernández Blasco, Esther Pastor, Jorge Abad-Capa, Josep María Montserrat, Valentín Cabriada-Nuño, Irene Cano-Pumarega, Jaime Corral-Peñafiel, Eva Arias, Olga Mediano, María Somoza-González, Joan Dalmau-Arias, Isaac Almendros, Ramón Farré, David Gozal, Francisco García-Río
Journal: European Respiratory Journal (2022)

In patients with obstructive sleep apnoea (OSA), intermittent hypoxia induces overexpression of paraspeckle component (PSPC)1, a master modulator of transforming growth factor (TGF)-β signalling, which promotes cell cancer progression through epithelial-mesenchymal transition (EMT) and acquisition of cancer stem cell (CSC)-like features. However, the persistence of intermittent hypoxia-induced effects on PSPC1, and their consequences in cancer patients are not known. To this effect, circulating PSPC1 levels were compared in patients with cutaneous melanoma with or without OSA, and their relationship with tumour aggressiveness along with the in vitro effects of soluble PSPC1 and intermittent hypoxia on melanoma cell aggressiveness mechanisms were assessed.In 292 cutaneous melanoma patients, sleep studies and serum levels of PSPC1 and TGF-β were evaluated. The effect of PSPC1 on expression of EMT and CSC transcription factors was assessed using melanoma cell lines with patient sera under both normoxia and intermittent hypoxia conditions.PSPC1 levels were higher in patients with moderate-severe OSA compared with mild OSA or non-OSA patients. Serum levels of PSPC1 were associated with several cutaneous melanoma clinical aggressiveness indicators. Both intermittent hypoxia exposures and serum from OSA patients upregulated TGF-β expression and amplified the expression of transcription factors associated with EMT activation and acquisition of CSC characteristics.In cutaneous melanoma patients, OSA severity is associated with higher PSPC1 serum levels, which jointly with intermittent hypoxia would enhance the self-reprogramming capabilities of EMT and CSC feature acquisition of melanoma cells, promoting their intrinsic aggressiveness.
Impact of academic medical center access on outcomes in multiple myeloma
Authors: Victoria A. Vardell, Daniel A. Ermann, Srinivas K. Tantravahi, Benjamin Haaland, Brian McClune, Amandeep Godara, Ghulam Rehman Mohyuddin, Douglas W. Sborov
Journal: American Journal of Hematology (2022)

Abstract Treatment at academic cancer centers (ACs) is associated with improved survival across hematologic malignancies, though the benefit in multiple myeloma (MM) has not been examined. This study aims to evaluate survival outcomes at Commission on Cancer accredited ACs compared to non‐academic centers (NACs) for patients receiving MM‐directed therapy. The National Cancer Database (NCDB) was used to identify demographics and overall survival (OS) of MM patients diagnosed from 2004 to 2017 and to compare outcomes by facility type. Survival analysis was repeated in a propensity score matched cohort, with NACs matched 1:1 to ACs by age, race, comorbidity score, insurance, year of diagnosis, distance traveled, and income. Of 163 375 MM patients, 44.5% were treated at ACs. Patients at ACs were more likely to receive MM‐directed therapy compared to NACs (81% vs. 73%, p &lt; .001). For patients receiving treatment, median OS at ACs was 71.3 months versus 41.2 months at NACs ( p &lt; .001). When adjusted for baseline demographics, patients treated at ACs had reduced mortality; hazard ratio (HR) 0.79 (95% CI 0.78–0.81, p &lt; .001). The propensity score matched cohort maintained this survival benefit with a median OS of 59.9 months at ACs versus 37.0 months at NACs ( p &lt; .001), HR of 0.66 (95% CI 0.64–0.67, p &lt; .001). ACs treated younger patients with fewer comorbidities and were more likely to treat racial minorities and patients with Medicaid or private insurance, and the uninsured. In this analysis, MM patients treated at ACs have significantly improved survival. While potentially related to access to specialized care, socioeconomic factors that drive facility selection may also contribute.
Reply to Xiangyang Yao, Chen Duan, Bo Li, Xiaoliang Wu and Hua Xu’s Letter to the Editor Re: Hilda A. de Barros, Matthias N. van Oosterom, Maarten L. Donswijk, et al. Robot-assisted Prostate-specific Membrane Antigen–radioguided Salvage Surgery in Recurrent Prostate Cancer Using a DROP-IN Gamma Probe: The First Prospective Feasibility Study. Eur Urol 2022;82:97–105
Authors: Hilda A. de Barros, Matthias N. van Oosterom, Maarten L. Donswijk, Jeroen J.M.A. Hendrikx, André N. Vis, Tobias Maurer, Fijs W.B. van Leeuwen, Henk G. van der Poel, Pim J. van Leeuwen
Journal: European Urology (2022)
Re: Jihad H. Kaouk, Ethan L. Ferguson, Alp Tuna Beksac, et al. Single-port Robotic Transvesical Partial Prostatectomy for Localized Prostate Cancer: Initial Series and Description of Technique. Eur Urol. 2022;82:551–58
Authors: Shangqing Ren, Xu Hu, Kai Wang, Qian Lv, Dong Wang
Journal: European Urology (2022)
Dual use of antifungals in medicine and agriculture: How do we help prevent resistance developing in human pathogens?
Authors: Paul E. Verweij, Maiken C. Arendrup, Ana Alastruey-Izquierdo, Jeremy A.W. Gold, Shawn R. Lockhart, Tom Chiller, P.Lewis White
Journal: Drug Resistance Updates (2022)

Azole resistance in Aspergillus fumigatus is a One Health resistance threat, where azole fungicide exposure compromises the efficacy of medical azoles. The use of the recently authorized fungicide ipflufenoquin, which shares its mode-of-action with a new antifungal olorofim, underscores the need for risk assessment for dual use of antifungals.
The role of bacteria and its derived biomaterials in cancer radiotherapy
Authors: Yu Zhang, Ruizhe Huang, Yunchun Jiang, Wenhao Shen, Hailong Pei, Guanglin Wang, Pei Pei, Kai Yang
Journal: Acta Pharmaceutica Sinica B (2022)

Bacteria-mediated anti-tumor therapy has received widespread attention due to its natural tumor-targeting ability and specific immune-activation characteristics. It has made significant progress in breaking the limitations of monotherapy and effectively eradicating tumors, especially when combined with traditional therapy, such as radiotherapy. According to their different biological characteristics, bacteria and their derivatives can not only improve the sensitivity of tumor radiotherapy but also protect normal tissues. Moreover, genetically engineered bacteria and bacteria-based biomaterials have further expanded the scope of their applications in radiotherapy. In this review, we have summarized relevant researches on the application of bacteria and its derivatives in radiotherapy in recent years, expounding that the bacteria, bacterial derivatives and bacteria-based biomaterials can not only directly enhance radiotherapy but also improve the anti-tumor effect by improving the tumor microenvironment (TME) and immune effects. Furthermore, some probiotics can also protect normal tissues and organs such as intestines from radiation via anti-inflammatory, anti-oxidation and apoptosis inhibition. In conclusion, the prospect of bacteria in radiotherapy will be very extensive, but its biological safety and mechanism need to be further evaluated and studied.
Upfront Cytoreductive Nephrectomy for Metastatic Renal Cell Carcinoma Treated with Immune Checkpoint Inhibitors or Targeted Therapy: An Observational Study from the International Metastatic Renal Cell Carcinoma Database Consortium
Authors: Ziad Bakouny, Talal El Zarif, Shaan Dudani, J. Connor Wells, Chun Loo Gan, Frede Donskov, Julia Shapiro, Ian D. Davis, Francis Parnis, Praful Ravi, John A. Steinharter, Neeraj Agarwal, Ajjai Alva, Lori Wood, Anil Kapoor, Jose M. Ruiz Morales, Christian Kollmannsberger, Benoit Beuselinck, Wanling Xie, Daniel Y.C. Heng, Toni K. Choueiri
Journal: European Urology (2022)
Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin
Authors: Deshka S. Foster, Michael Januszyk, Daniel Delitto, Kathryn E. Yost, Michelle Griffin, Jason Guo, Nicholas Guardino, Andrea E. Delitto, Malini Chinta, Austin R. Burcham, Alan T. Nguyen, Khristian E. Bauer-Rowe, Ashley L. Titan, Ankit Salhotra, R. Ellen Jones, Oscar da Silva, Hunter G. Lindsay, Charlotte E. Berry, Kellen Chen, Dominic Henn, Shamik Mascharak, Heather E. Talbott, Alexia Kim, Fatemeh Nosrati, Dharshan Sivaraj, R. Chase Ransom, Michael Matthews, Anum Khan, Dhananjay Wagh, John Coller, Geoffrey C. Gurtner, Derrick C. Wan, Irene L. Wapnir, Howard Y. Chang, Jeffrey A. Norton, Michael T. Longaker
Journal: Cancer Cell (2022)
AAV-mediated gene therapy produces fertile offspring in the Lhcgr-deficient mouse model of Leydig cell failure
Authors: Kai Xia, Fulin Wang, Xingqiang Lai, Lin Dong, Peng Luo, Suyuan Zhang, Cuifeng Yang, Hong Chen, Yuanchen Ma, Weijun Huang, Wangsheng Ou, Yuyan Li, Xin Feng, Bin Yang, Congyuan Liu, Zhenmin Lei, Xiang’an Tu, Qiong Ke, Frank Fuxiang Mao, Chunhua Deng, Andy Peng Xiang
Journal: Cell Reports Medicine (2022)

Leydig cell failure (LCF) caused by gene mutation results in testosterone deficiency and infertility. Serum testosterone levels can be recovered via testosterone replacement; however, established therapies have shown limited success in restoring fertility. Here, we use a luteinizing hormone/choriogonadotrophin receptor (Lhcgr)-deficient mouse model of LCF to investigate the feasibility of gene therapy for restoring testosterone production and fertility. We screen several adeno-associated virus (AAV) serotypes and identify AAV8 as an efficient vector to drive exogenous Lhcgr expression in progenitor Leydig cells through interstitial injection. We observe considerable testosterone recovery and Leydig cell maturation after AAV8-Lhcgr treatment in pubertal Lhcgr−/− mice. Of note, this gene therapy partially recovers sexual development, substantially restores spermatogenesis, and effectively produces fertile offspring. Furthermore, these favorable effects can be reproduced in adult Lhcgr−/− mice. Our proof-of-concept experiments in the mouse model demonstrate that AAV-mediated gene therapy may represent a promising therapeutic approach for patients with LCF.
Meningococcal disease in North America: Updates from the Global Meningococcal Initiative
Authors: Edwin J. Asturias, Xilian Bai, Julie A. Bettinger, Ray Borrow, Delia Nais Castillo, Dominique A. Caugant, Grettel Chanto Chacon, Ener Cagri Dinleyici, Gabriela Echaniz-Aviles, Luis Garcia, Linda Glennie, Lee H. Harrison, Rebecca L. Howie, Mark Itsko, Jay Lucidarme, Jose Eduardo Oliva Marin, Henju Marjuki, Lucy A. McNamara, Mustapha M. Mustapha, Joan L. Robinson, Belkis Romeu, Manish Sadarangani, Xavier Sáez-Llorens, Marco A.P. Sáfadi, David S. Stephens, James M. Stuart, Muhamed-Kheir Taha, Raymond S.W. Tsang, Julio Vazquez, Philippe De Wals
Journal: Journal of Infection (2022)
The changing epidemiology of PIMS-TS across COVID-19 waves: prospective national surveillance, January 2021 to July 2022, England
Authors: Joseph Shingleton, Hannah Williams, Godwin Oligbu, Annabel Powell, Jonathan Cohen, Moshe Arditi, Tiffany Watson-Koszel, Simon Kenny, Nick Gent, Shamez N Ladhani
Journal: Journal of Infection (2022)
Breakthrough infection shapes humoral immunity against SARS-CoV-2 Omicron Variant
Authors: Yuwei Zhang, Shanshan Han, Xingyu Guo, Mingxiao Yao, Lianxiang Zhao, Wenkui Sun, Shuang Wang, Bo Pang, Shu Zhang, Jianxing Wang, Ming Fang, Xiaolin Liu, Zengqiang Kou, Xiaolin Jiang
Journal: Journal of Infection (2022)
Long noncoding TSI attenuates aortic valve calcification by suppressing TGF-β1-induced osteoblastic differentiation of valve interstitial cells
Authors: Zongtao Liu, Yixuan Wang, Fayuan Liu, Da Zhu, Yuqi Chen, Wei Yen Yim, Ke Hu, Zhenqi Rao, Xiangbin Pan, Fei Li, Nianguo Dong
Journal: Metabolism (2022)